build based on 1e3147b

COBREXA · Dec 9, 2023 · fc8507c · fc8507c
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diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-12-09T21:08:40","documenter_version":"1.2.1"}}
+{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-12-09T21:53:39","documenter_version":"1.2.1"}}
diff --git a/dev/canonical/index.html b/dev/canonical/index.html
@@ -107,18 +107,18 @@
 A.gene_notes(m::Model, id::String) = m.genes[id].notes
 
 function A.stoichiometry(m::Model)
-    midxs = Dict(mid =&gt; idx for (idx, (mid, _)) in enumerate(m.metabolites))
+    midxs = Dict(mid =&gt; idx for (idx, mid) in enumerate(A.metabolites(m)))
     I = Int[]
     J = Int[]
     V = Float64[]
-    for (ridx, (_, r)) in enumerate(m.reactions)
-        for (smid, v) in r.stoichiometry
+    for (ridx, rid) in enumerate(A.reactions(m))
+        for (smid, v) in m.reactions[rid].stoichiometry
             push!(I, midxs[smid])
             push!(J, ridx)
             push!(V, v)
         end
     end
-    sparse(I, J, V, length(m.metabolites), length(m.reactions))
+    sparse(I, J, V, A.n_metabolites(m), A.n_reactions(m))
 end
 
 A.bounds(m::Model) = (
@@ -235,4 +235,4 @@
     A.save(m, path)
     A.run_fbcmodel_file_tests(Model, path, name = &quot;small model&quot;)
 end;</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi"><span class="sgr1">Test Summary:                                                      | <span class="sgr32">Pass  </span><span class="sgr36">Total  </span>Time</span>
-Model `small model&#39; of type AbstractFBCModels.CanonicalModel.Model | <span class="sgr32">  45  </span><span class="sgr36">   45  </span>0.1s</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« README</a><a class="docs-footer-nextpage" href="../utilities/">Utility functions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Saturday 9 December 2023 21:08">Saturday 9 December 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+Model `small model&#39; of type AbstractFBCModels.CanonicalModel.Model | <span class="sgr32">  45  </span><span class="sgr36">   45  </span>0.1s</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« README</a><a class="docs-footer-nextpage" href="../utilities/">Utility functions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Saturday 9 December 2023 21:53">Saturday 9 December 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>